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Posted to dev@ctakes.apache.org by Lani Lin <li...@informatik.uni-leipzig.de> on 2017/03/28 14:49:41 UTC
SenseDisambiguatorAnnotator in ctakes 4.0?
Hi,
Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still
be only part of ytex?
best,
Lani
Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by James Masanz <ma...@gmail.com>.
fwiw, the only change to ytex I am making for 4.0 is what is necessary for
updating hsqldb to 2.3.4
On Wed, Mar 29, 2017 at 10:02 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Lani,
>
> Great questions. As far as I know nobdy is changing what is in ytex for
> this release. So, if you run the default ctakes clinical pipeline the rare
> word lookup will be used. If you run ytex then the old first word will
> still be used.
>
> The gui does not support first word lookup. Somebody may add that in the
> future (there actually is code in sandbox), but I don't plan to do it
> myself.
>
> Sean
>
>
>
>
> -----Original Message-----
> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> Sent: Wednesday, March 29, 2017 9:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi Sean,
>
> thanks. Will the new dictionary building GUI also include building
> dictionaries for first word lookup?
>
> Another question to be clarified: if the dictionary used in ctakes FIRST
> word also the same as YTEX?
>
> In other words, if the results from ctakes FIRST word = those from YTEX?
>
> best,
>
> Lani
>
>
> On 29.03.2017 15:23, Finan, Sean wrote:
> > Hi Lani,
> >
> > The rare word lookup will be the default. The default redistributable
> dictionary will be umls snomed and rxnorm 2016ab.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> > Sent: Wednesday, March 29, 2017 3:27 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
> >
> > Hi Sean,
> >
> > thanks for your reply. I'll try to make the annotator running and see if
> I can do more.
> >
> > Another question regarding ctakes 4.0, will it use the first word or
> rare word algorithm?
> >
> > best,
> >
> > Lani
> >
> >
> > On 28.03.2017 17:23, Finan, Sean wrote:
> >> Hi Lani,
> >>
> >> It will remain part of the ytex package. There is some effort being
> made toward getting new wsd into ctakes, but it will not be introduced for
> some time.
> >>
> >> If anybody out there has something that they would like to contribute
> to ctakes, please do!
> >>
> >> Sean
> >>
> >> -----Original Message-----
> >> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> >> Sent: Tuesday, March 28, 2017 10:50 AM
> >> To: dev@ctakes.apache.org
> >> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
> >>
> >> Hi,
> >>
> >> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will
> still be only part of ytex?
> >>
> >> best,
> >> Lani
> >>
> >>
> > --
> > Ying-Chi Lin
> > (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig
> > .de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> > SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2U738MxWz
> > u_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ&s=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF
> > 3f1dASrCN0&e= ) Database Group, Department of Computer Science,
> > Universität Leipzig
> >
> >
>
> --
> Ying-Chi Lin (https://urldefense.proofpoint.com/v2/url?u=http-
> 3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin&d=DwIDaQ&
> c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=t_
> U9PuQaNHQ2VM8FIstsF4ug7xjcOdgug7Mg3GMZYZw&s=PdaX792dIQZYHdBURxYgyRLftyxqEP
> aP5GXCl8oFpw8&e= ) Database Group, Department of Computer Science,
> Universität Leipzig
>
>
Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by Lani Lin <li...@informatik.uni-leipzig.de>.
Hi Sean,
thanks for the clarification. To conclude, the new ctakes 4.0 will be an
update for the fast version.
YTEX is the extension of the old first word version. In this case, YTEX
has already provided dictionary building function and in addition, the
SenseDisambiguatorAnnotator.
I will be testing these two versions (fast and YTEX) on medical forms.
Will come back to report the comparison later.
best,
Lani
On 29.03.2017 16:02, Finan, Sean wrote:
> Hi Lani,
>
> Great questions. As far as I know nobdy is changing what is in ytex for this release. So, if you run the default ctakes clinical pipeline the rare word lookup will be used. If you run ytex then the old first word will still be used.
>
> The gui does not support first word lookup. Somebody may add that in the future (there actually is code in sandbox), but I don't plan to do it myself.
>
> Sean
>
>
>
>
> -----Original Message-----
> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> Sent: Wednesday, March 29, 2017 9:59 AM
> To: dev@ctakes.apache.org
> Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi Sean,
>
> thanks. Will the new dictionary building GUI also include building dictionaries for first word lookup?
>
> Another question to be clarified: if the dictionary used in ctakes FIRST word also the same as YTEX?
>
> In other words, if the results from ctakes FIRST word = those from YTEX?
>
> best,
>
> Lani
>
>
> On 29.03.2017 15:23, Finan, Sean wrote:
>> Hi Lani,
>>
>> The rare word lookup will be the default. The default redistributable dictionary will be umls snomed and rxnorm 2016ab.
>>
>> Sean
>>
>> -----Original Message-----
>> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
>> Sent: Wednesday, March 29, 2017 3:27 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
>>
>> Hi Sean,
>>
>> thanks for your reply. I'll try to make the annotator running and see if I can do more.
>>
>> Another question regarding ctakes 4.0, will it use the first word or rare word algorithm?
>>
>> best,
>>
>> Lani
>>
>>
>> On 28.03.2017 17:23, Finan, Sean wrote:
>>> Hi Lani,
>>>
>>> It will remain part of the ytex package. There is some effort being made toward getting new wsd into ctakes, but it will not be introduced for some time.
>>>
>>> If anybody out there has something that they would like to contribute to ctakes, please do!
>>>
>>> Sean
>>>
>>> -----Original Message-----
>>> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
>>> Sent: Tuesday, March 28, 2017 10:50 AM
>>> To: dev@ctakes.apache.org
>>> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>>>
>>> Hi,
>>>
>>> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be only part of ytex?
>>>
>>> best,
>>> Lani
>>>
>>>
>> --
>> Ying-Chi Lin
>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig
>> .de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
>> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2U738MxWz
>> u_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ&s=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF
>> 3f1dASrCN0&e= ) Database Group, Department of Computer Science,
>> Universit�t Leipzig
>>
>>
> --
> Ying-Chi Lin (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=t_U9PuQaNHQ2VM8FIstsF4ug7xjcOdgug7Mg3GMZYZw&s=PdaX792dIQZYHdBURxYgyRLftyxqEPaP5GXCl8oFpw8&e= ) Database Group, Department of Computer Science, Universit�t Leipzig
>
>
--
Ying-Chi Lin (http://dbs.uni-leipzig.de/de/person/yingchi_lin)
Database Group, Department of Computer Science, Universit�t Leipzig
RE: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Lani,
Great questions. As far as I know nobdy is changing what is in ytex for this release. So, if you run the default ctakes clinical pipeline the rare word lookup will be used. If you run ytex then the old first word will still be used.
The gui does not support first word lookup. Somebody may add that in the future (there actually is code in sandbox), but I don't plan to do it myself.
Sean
-----Original Message-----
From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
Sent: Wednesday, March 29, 2017 9:59 AM
To: dev@ctakes.apache.org
Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Hi Sean,
thanks. Will the new dictionary building GUI also include building dictionaries for first word lookup?
Another question to be clarified: if the dictionary used in ctakes FIRST word also the same as YTEX?
In other words, if the results from ctakes FIRST word = those from YTEX?
best,
Lani
On 29.03.2017 15:23, Finan, Sean wrote:
> Hi Lani,
>
> The rare word lookup will be the default. The default redistributable dictionary will be umls snomed and rxnorm 2016ab.
>
> Sean
>
> -----Original Message-----
> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> Sent: Wednesday, March 29, 2017 3:27 AM
> To: dev@ctakes.apache.org
> Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi Sean,
>
> thanks for your reply. I'll try to make the annotator running and see if I can do more.
>
> Another question regarding ctakes 4.0, will it use the first word or rare word algorithm?
>
> best,
>
> Lani
>
>
> On 28.03.2017 17:23, Finan, Sean wrote:
>> Hi Lani,
>>
>> It will remain part of the ytex package. There is some effort being made toward getting new wsd into ctakes, but it will not be introduced for some time.
>>
>> If anybody out there has something that they would like to contribute to ctakes, please do!
>>
>> Sean
>>
>> -----Original Message-----
>> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
>> Sent: Tuesday, March 28, 2017 10:50 AM
>> To: dev@ctakes.apache.org
>> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>>
>> Hi,
>>
>> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be only part of ytex?
>>
>> best,
>> Lani
>>
>>
> --
> Ying-Chi Lin
> (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig
> .de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2U738MxWz
> u_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ&s=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF
> 3f1dASrCN0&e= ) Database Group, Department of Computer Science,
> Universität Leipzig
>
>
--
Ying-Chi Lin (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=t_U9PuQaNHQ2VM8FIstsF4ug7xjcOdgug7Mg3GMZYZw&s=PdaX792dIQZYHdBURxYgyRLftyxqEPaP5GXCl8oFpw8&e= ) Database Group, Department of Computer Science, Universität Leipzig
Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by Lani Lin <li...@informatik.uni-leipzig.de>.
Hi Sean,
thanks. Will the new dictionary building GUI also include building
dictionaries for first word lookup?
Another question to be clarified: if the dictionary used in ctakes FIRST
word also the same as YTEX?
In other words, if the results from ctakes FIRST word = those from YTEX?
best,
Lani
On 29.03.2017 15:23, Finan, Sean wrote:
> Hi Lani,
>
> The rare word lookup will be the default. The default redistributable dictionary will be umls snomed and rxnorm 2016ab.
>
> Sean
>
> -----Original Message-----
> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> Sent: Wednesday, March 29, 2017 3:27 AM
> To: dev@ctakes.apache.org
> Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi Sean,
>
> thanks for your reply. I'll try to make the annotator running and see if I can do more.
>
> Another question regarding ctakes 4.0, will it use the first word or rare word algorithm?
>
> best,
>
> Lani
>
>
> On 28.03.2017 17:23, Finan, Sean wrote:
>> Hi Lani,
>>
>> It will remain part of the ytex package. There is some effort being made toward getting new wsd into ctakes, but it will not be introduced for some time.
>>
>> If anybody out there has something that they would like to contribute to ctakes, please do!
>>
>> Sean
>>
>> -----Original Message-----
>> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
>> Sent: Tuesday, March 28, 2017 10:50 AM
>> To: dev@ctakes.apache.org
>> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>>
>> Hi,
>>
>> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be only part of ytex?
>>
>> best,
>> Lani
>>
>>
> --
> Ying-Chi Lin (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2U738MxWzu_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ&s=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF3f1dASrCN0&e= ) Database Group, Department of Computer Science, Universit�t Leipzig
>
>
--
Ying-Chi Lin (http://dbs.uni-leipzig.de/de/person/yingchi_lin)
Database Group, Department of Computer Science, Universit�t Leipzig
RE: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Lani,
The rare word lookup will be the default. The default redistributable dictionary will be umls snomed and rxnorm 2016ab.
Sean
-----Original Message-----
From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
Sent: Wednesday, March 29, 2017 3:27 AM
To: dev@ctakes.apache.org
Subject: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Hi Sean,
thanks for your reply. I'll try to make the annotator running and see if I can do more.
Another question regarding ctakes 4.0, will it use the first word or rare word algorithm?
best,
Lani
On 28.03.2017 17:23, Finan, Sean wrote:
> Hi Lani,
>
> It will remain part of the ytex package. There is some effort being made toward getting new wsd into ctakes, but it will not be introduced for some time.
>
> If anybody out there has something that they would like to contribute to ctakes, please do!
>
> Sean
>
> -----Original Message-----
> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> Sent: Tuesday, March 28, 2017 10:50 AM
> To: dev@ctakes.apache.org
> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi,
>
> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be only part of ytex?
>
> best,
> Lani
>
>
--
Ying-Chi Lin (https://urldefense.proofpoint.com/v2/url?u=http-3A__dbs.uni-2Dleipzig.de_de_person_yingchi-5Flin&d=DwIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=2U738MxWzu_mmcrY00IpwCh3R-URXYCLMzY91aNSMWQ&s=f_-F5l58L6ao70tJDeJOk0etiYbuplvGF3f1dASrCN0&e= ) Database Group, Department of Computer Science, Universität Leipzig
Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by Lani Lin <li...@informatik.uni-leipzig.de>.
Hi Sean,
thanks for your reply. I'll try to make the annotator running and see if
I can do more.
Another question regarding ctakes 4.0, will it use the first word or
rare word algorithm?
best,
Lani
On 28.03.2017 17:23, Finan, Sean wrote:
> Hi Lani,
>
> It will remain part of the ytex package. There is some effort being made toward getting new wsd into ctakes, but it will not be introduced for some time.
>
> If anybody out there has something that they would like to contribute to ctakes, please do!
>
> Sean
>
> -----Original Message-----
> From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
> Sent: Tuesday, March 28, 2017 10:50 AM
> To: dev@ctakes.apache.org
> Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
>
> Hi,
>
> Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be only part of ytex?
>
> best,
> Lani
>
>
--
Ying-Chi Lin (http://dbs.uni-leipzig.de/de/person/yingchi_lin)
Database Group, Department of Computer Science, Universit�t Leipzig
RE: SenseDisambiguatorAnnotator in ctakes 4.0?
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Lani,
It will remain part of the ytex package. There is some effort being made toward getting new wsd into ctakes, but it will not be introduced for some time.
If anybody out there has something that they would like to contribute to ctakes, please do!
Sean
-----Original Message-----
From: Lani Lin [mailto:lin@informatik.uni-leipzig.de]
Sent: Tuesday, March 28, 2017 10:50 AM
To: dev@ctakes.apache.org
Subject: SenseDisambiguatorAnnotator in ctakes 4.0?
Hi,
Will the ctakes 4.0 include SenseDisambiguatorAnnotator or it will still be only part of ytex?
best,
Lani